The European Nucleotide Archive in 2018

Harrison, Peter W.; Alako, Blaise T. F.; Amid, Clara; Cerdeño-Tárraga, Ana; Cleland, Ian; Holt, Sam; Hussein, Abdulrahman; Jayathilaka, Suran; Kay, Simon; Keane, Thomas M.; Leinonen, Rasko; Xin, Liu; Martínez-Villacorta, Josué; Milano, Annalisa; Pakseresht, Nima; Rajan, Jeena; Reddy, Kethi; Richards, E. G.; Rosello, Marc; Silvester, Nicole C.; Smirnov, Dmitriy; Toribio, Ana-Luisa; Vijayaraja, Senthilnathan; Cochrane, Guy

doi:10.1093/nar/gky1078

Cited by 99 publications

(64 citation statements)

References 11 publications

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“…Protein sequences were obtained from the UniProtKB database (43) with the maximal-protein-evidence-level set to 4, including only reviewed Swiss-Prot entries. The mRNA coding sequences for each protein were downloaded from the European Nucleotide Archive Database (44). Sequences including non-canonical amino acids or nucleobases were not analyzed.…”

Section: Methodsmentioning

confidence: 99%

Invariants of Frameshifted Variants

Bartonek

Braun

Žagrović

2019

Preprint

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Frameshifts in protein coding sequences are widely perceived as resulting in either non-functional or even deleterious protein products. Indeed, frameshifts typically lead to markedly altered protein sequences and premature stop codons. By analyzing complete proteomes from all three domains of life, we demonstrate that, in contrast, several key physicochemical properties of protein sequences exhibit significant robustness against +1 and −1 frameshifts in their mRNA coding sequences. In particular, we show that hydrophobicity profiles of many protein sequences remain largely invariant upon frameshifting. For example, over 2900 human proteins exhibit a Pearson correlation coefficient between the hydrophobicity profiles of the original and the +1-frameshifted variants greater than 0.7, despite a median sequence identity between the two of only 6.5% in this group. We observe a similar effect for protein sequence profiles of affinity for certain nucleobases, their matching with the cognate mRNA nucleobase-density profiles as well as protein sequence profiles of intrinsic disorder. Finally, we show that frameshift invariance is directly embedded in the structure of the universal genetic code and may have contributed to shaping it. Our results suggest that frameshifting may be a powerful evolutionary mechanism for creating new proteins with vastly different sequences, yet similar physicochemical properties to the proteins they originate from.Significance StatementGenetic information stored in DNA is transcribed to messenger RNAs and then read in the process of translation to produce proteins. A frameshift in the reading frame at any stage of the process typically results in a significantly different protein sequence being produced and is generally assumed to be a source of detrimental errors that biological systems need to control. Here, we show that several essential properties of many protein sequences, such as their hydrophobicity profiles, remain largely unchanged upon frameshifts. This finding suggests that frameshifting could be an effective evolutionary strategy for generating novel protein sequences, which retain the functionally relevant physicochemical properties of the sequences they derive from.

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Section: Methodsmentioning

confidence: 99%

Invariants of Frameshifted Variants

Bartonek

Braun

Žagrović

2019

Preprint

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“…The limitations can be addressed and new functionalities added in the future. For instance, different bioinformatics datasets like Ensembl [7] or ENA [8] can be integrated. Another feature would be sorting result values based on a certain criterion.…”

Section: Future Workmentioning

confidence: 99%

“…Based on stored data, Biobtree provides search, map and visualization functionalities via provided web services or a web interface. For instance, all the UniProt proteins entries belonging to a gene name, or, all Ensembl [7] genome transcripts identifiers and ENA [8] sequence identifiers that map to a protein identifier can be accessed. These relations, determined via identifiers, are stored bidirectionally so all actions can also be done in the opposite way.…”

Section: Introductionmentioning

confidence: 99%

Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords

Gur

2019

Preprint

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Due to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manual or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the growing volume of bioinformatics datasets, emerging new software tools and approaches motivates new solutions. To provide a new tool for these current cases, I present the Biobtree bioinformatics tool. Biobtree effectively fetches and indexes identifiers and special keywords with their related identifiers from supported datasets, optionally with user pre-defined datasets and provides a web interface, web services and direct B+ tree data structure-based single uniform database output. Biobtree can handle billions of identifiers and runs via a single executable file with no installation and dependency required. It also aims to provide a relatively small codebase for easy maintenance, addition of new features and extension to larger datasets. Biobtree is available to download at https://www.github.com/tamerh/biobtree.

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“…The major database with these characteristics is the Sequencing Read Archive (SRA) (2). SRA is part of the International Nucleotide Sequence Database Collaboration (3) along with the European Nucleotide Archive (4) and the DNA Data Bank of Japan (5). Another important repository is MG-RAST (6), which also provides analysis services.…”

Section: Introductionmentioning

confidence: 99%

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

Corrêa

Saraiva

Stadler

et al. 2019

Preprint

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2Microbiome studies focused on the genetic potential of microbial communities (metagenomics) 1 3 became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the 1 4 two main metagenome repositories, contain over 202 858 public available metagenomes and this 1 5 number has increased exponentially. However, mining databases can be challenging due to 1 6 misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to 1 7 make it easier for scientists to find terrestrial metagenomes of interest that could be compared with 1 8 novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to 1 9

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The European Nucleotide Archive in 2018

Cited by 99 publications

References 11 publications

Invariants of Frameshifted Variants

Invariants of Frameshifted Variants

Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

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